@apollo-annotation/mst 0.3.1 → 0.3.3

package/package.json

@@ -1,12 +1,12 @@
 {
   "name": "@apollo-annotation/mst",
-  "version": "0.3.1",
+  "version": "0.3.3",
   "main": "./dist/index.js",
   "scripts": {
     "build": "tsc"
   },
   "dependencies": {
-    "@jbrowse/core": "^2.13.1",
+    "@jbrowse/core": "^3.0.1",
     "mobx": "^6.6.1",
     "mobx-state-tree": "^5.4.0",
     "react-dom": "^18.2.0",

package/src/AnnotationFeatureModel.ts

@@ -1,4 +1,4 @@
-import { intersection2 } from '@jbrowse/core/util'
+import { getSession, intersection2 } from '@jbrowse/core/util'
 import {
   IAnyModelType,
   IMSTMap,
@@ -127,20 +127,28 @@ export const AnnotationFeatureModel = types
       return false
     },
     get transcriptParts(): TranscriptParts[] {
-      if (self.type !== 'mRNA') {
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-explicit-any
+      const session = getSession(self) as any
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+      const { apolloDataStore } = session
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access
+      const { featureTypeOntology } = apolloDataStore.ontologyManager
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+      if (!featureTypeOntology.isTypeOf(self.type, 'transcript')) {
         throw new Error(
-          'Only features of type "mRNA" or equivalent can calculate CDS locations',
+          'Only features of type "transcript" or equivalent can calculate CDS locations',
         )
       }
       const children = self.children as Children
       if (!children) {
-        throw new Error('no CDS or exons in mRNA')
+        throw new Error('no CDS or exons in transcript')
       }
       const cdsChildren = [...children.values()].filter(
-        (child) => child.type === 'CDS',
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+        (child) => featureTypeOntology.isTypeOf(child.type, 'CDS'),
       )
       if (cdsChildren.length === 0) {
-        throw new Error('no CDS in mRNA')
+        throw new Error('no CDS in transcript')
       }
       const transcriptParts: TranscriptParts[] = []
       for (const cds of cdsChildren) {
@@ -149,7 +157,8 @@ export const AnnotationFeatureModel = types
         let hasIntersected = false
         const exonLocations: TranscriptPartLocation[] = []
         for (const [, child] of children) {
-          if (child.type === 'exon') {
+          // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+          if (featureTypeOntology.isTypeOf(child.type, 'exon')) {
             exonLocations.push({ min: child.min, max: child.max })
           }
         }